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Machine learning (ML) potentials are a powerful tool in molecular modeling, enabling ab initio accuracy for comparably small computational costs. Nevertheless, all-atom simulations employing best-performing graph neural network…
The dynamics of the electrons for a molecule in solution is coupled to the dynamics of its polarizable environment, i.e., the solvent. To theoretically investigate such electronic dynamics, we have recently developed equations of motion…
We present LayerPCM, an extension of the polarizable-continuum model coupled to real-time time-dependent density-functional theory for an efficient and accurate description of the electrostatic interactions between molecules and…
The Poisson-Boltzmann (PB) implicit solvent model is a popular framework for studying the electrostatics of biomolecules immersed in water with dissolved salt. In this model the dielectric interface between the biomolecule and solvent is…
The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is…
Implicit solvent models, such as Poisson-Boltzmann models, play important roles in computational studies of biomolecules. A vital step in almost all implicit solvent models is to determine the solvent-solute interface, and the solvent…
We address in this thesis the current need to design new parallel algorithms and tools that ease the development of geodynamic modelling applications that are suited for today's and tomorrow's hardware. We present (1) the MATLAB HPC…
Earlier, normalization conditions for the columns of the PCM (Polarized Continuum Model) were determined and a method of enlarged surface meshes was developed. We developed similar methods for the COSMO (COnductor like Screening MOdel).…
In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
The sample-based quantum diagonalization (SQD) method shows great promise in quantum-centric simulations of ground state energies in molecular systems. Inclusion of solute-solvent interactions in simulations of electronic structure is…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
The AGBNP2 implicit solvent model, an evolution of the Analytical Generalized Born plus Non-Polar (AGBNP) model we have previously reported, is presented with the aim of modeling hydration effects beyond those described by conventional…
Implicit solvent models (ISMs) promise to deliver the accuracy of explicit solvent simulations at a fraction of the computational cost. However, despite decades of development, their accuracy has remained insufficient for many critical…
Molecular dynamics (MD) simulations enable the study of the motion of small and large (bio)molecules and the estimation of their conformational ensembles. The description of the environment (solvent) has thereby a large impact. Implicit…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…
Accurate and efficient prediction of multi-scale flows remains a formidable challenge. Constructing theoretical models and numerical methods often involves the design and optimization of parameters. While gradient descent methods have been…
A hallmark of meso-scale interfacial fluids is the multi-faceted, scale-dependent interfacial energy, which often manifests different characteristics across the molecular and continuum scale. The multi-scale nature imposes a challenge to…
This paper proposes a sign gradient descent (SGD) algorithm for predicting the three-dimensional folded protein molecule structures under the kinetostatic compliance method (KCM). In the KCM framework, which can be used to simulate the…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
In this article, we apply the binary level set method to the Variational Implicit Solvent Model (VISM), which is a theoretical and computational tool to study biomolecular systems with complex topology. Central in VISM is an effective free…